Details of assembly methods and in silico genotyping for Salmonella

  • All MLST-like typing methods in EnteroBase are derived from a genome assembly of sequenced reads. For an explanation of this method, see here

  • For a general description of the in silico typing method, see here

MLST – Classic

Ribosomal MLST (Jolley, 2012)

Core Genome MLST

Whole Genome MLST

7 Loci

51 Loci

3,002 Loci

21,065 Loci

Conserved Housekeeping genes

Ribosomal proteins

Core genes

Any coding sequence

Highly conserved; Low resolution

Highly conserved; Medium resolution

Variable; High resolution

Highly variable; Extreme resolution

Different scheme for each species/genus

Single scheme across tree of life

Different scheme for each species/genus

Different scheme for each species/genus

7 Gene MLST

Classic MLST scheme is described in Kidgell et al (2002) Infection, Genetics and Evolution. 2(1) 39-45.

Genes included in 7 gene MLST (together with the length of sequence used for MLST taken from table 1 in the above cited paper):

Gene

Name/ Locus Tag

Length

thrA

STY0002

501

purE

STY0582

399

sucA

STY0779

501

hisD

STY2281

501

aroC

STY2616

501

hemD

STY3622

432

dnaN

STY3941

501

Ribosomal MLST (rMLST)